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A federal judge in Boston struck a blow to the Defense of Marriage Act on Thursday by ruling in favor of married same-sex couples seeking federal-based benefits.

U.S. District Court Judge Joseph Tauro said in a 44-page decision that states, not the federal government, had the final say in defining marriage. Same-sex marriage became legal in Massachusetts in 2004, eight years after President Clinton signed the federal DOMA into law.

The judge also ruled that Section 3 of DOMA, which defines marriage as between one man and one woman for purposes of federal law, violated equal protection principles of the Constitution.

“In the wake of DOMA, it is only sexual orientation that differentiates a married couple entitled to federal marriage-based benefits from one not so entitled,” said Judge Tauro in his decision. “And this court can conceive of no way in which such a difference might be relevant to the provision of the benefits at issue.”

Court watchers predicted the ruling would be appealed before the U.S. Court of Appeals for the First Circuit. A Justice Department spokeswoman said Thursday the decision was under review.

Whether the Obama administration would vigorously defend the law was called into question by conservatives. President Obama has spoken out in favor of same-sex marriage.

“In part, this decision results from the deliberately weak legal defense of DOMA that was mounted on behalf of the government by the Obama administration, which has called for repeal of the law,” Tom McClusky, senior vice president of the Family Research Council, said in a statement.

“While the American people have made it unmistakably clear that they want to preserve marriage as the legal union of one man and one woman, liberals and activist judges are not content to let the people decide,” he said.

Joe Solmonese, president of the Human Rights Campaign, a gay-rights advocacy organization, praised the judge’s decision, calling it “an important step forward.”

“Today’s decision is a confirmation of what every lesbian, gay, bisexual and transgender American knows to be a basic truth - we, and our families, are equal,” Mr. Solmonese said in a statement.

He also urged the Obama administration to “push Congress to repeal a law that we know, and Judge Tauro recognized, serves no purpose but to denigrate our families.”

While the ruling covers only Massachusetts, critics worried that the legal precedent would be used by other plaintiffs seeking to overturn the federal law.

“It’s another example of a judge usurping the authority of Congress,” said Brian Raum, senior counsel for the conservative Alliance Defense Fund. “At this point the court only has jurisdiction over Massachusetts, but this may embolden those in other jurisdictions to file their own lawsuits.”

The District of Columbia and six states - Massachusetts, Connecticut, Iowa, Vermont, Maine and New Hampshire - have legalized same-sex marriage, while another 30 states have approved their own Defense of Marriage acts. A ruling is expected soon in a federal challenge to California’s Proposition 8, which upholds traditional marriage and was approved by voters in 2008.

The Massachusetts lawsuit was filed on behalf of eight same-sex couples seeking federal benefits available to heterosexual couples and three surviving gay spouses who had been denied survivors’ benefits under DOMA.

The state had also filed its own lawsuit challenging the federal statute.